MvpResults: model evaluation and feature visualization

Given that an appropriate Mvp-object exists, it is really easy to implement a machine learning analysis using standard scikit-learn modules. However, as fMRI datasets are often relatively small, K-fold cross-validation is often performed to keep the training-set as large as possible. Additionally, it might be informative to visualize which features are used and are most important in your model. (But, note that feature mapping should not be the main objective of decoding analyses!) Doing this - model evaluation and feature visualization across multiple folds - complicates the process of implementing machine learning pipelines on fMRI data.

The MvpResults object offers a solution to the above complications. Simply pass your scikit-learn pipeline to MvpResults after every fold and it automatically calculates a set of model evaluation metrics (accuracy, precision, recall, etc.) and keeps track of which features are used and how ‘important’ these features are (in terms of the value of their weights).

Feature selection/extraction

The feature_selection and feature_extraction modules in skbold contain a set of scikit-learn type transformers that can perform various types of feature selection and extraction specific to multivoxel fMRI-data. For example, the RoiIndexer-transformer takes a (partially masked) whole-brain pattern and indexes it with a specific region-of-interest defined in a nifti-file. The transformer API conforms to scikit-learn transformers, and as such, (almost all of them) can be used in scikit-learn pipelines.

To get a better idea of the package’s functionality - including the use of Mvp-objects, transformers, and MvpResults - a typical analysis workflow using skbold is described below.

For some example usages of the Mvp-objects and how to incorporate them in a scikit-learn-based ML-pipeline, check the examples below:

An example workflow: MvpWithin

Suppose you have data from an fMRI-experiment for a set of subjects who were presented with images which were either emotional or neutral in terms of their content. You’ve modelled them using a single-trial GLM (i.e. each trial is modelled as a separate event/regressor) and calculated their corresponding contrasts against baseline. The resulting FEAT-directory then contains a directory (‘stats’) with contrast-estimates (COPEs) for each trial. Now, using MvpWithin, it is easy to extract a sample by features matrix and some meta-data associated with it, as shown below.

from skbold.core import MvpWithin

feat_dir = '~/project/sub001.feat'
mask_file = '~/GrayMatterMask.nii.gz' # mask all non-gray matter!
read_labels = True # parse labels (targets) from design.con file!
remove_contrast = ['nuisance_regressor_x'] # do not load nuisance regressor!
ref_space = 'epi' # extract patterns in functional space (alternatively: 'mni')
statistic = 'tstat' # use the tstat*.nii.gz files (in *.feat/stats) as patterns
remove_zeros = True # remove voxels which are zero in each trial

mvp = MvpWithin(source=feat_dir, read_labels=read_labels,
                remove_contrast=remove_contrast, ref_space=ref_space,
                statistic=statistic, remove_zeros=remove_zeros,

mvp.create() # extracts and stores (meta)data from FEAT-directory!
mvp.write(path='~/', name='mvp_sub001') # saves to disk!

Now, we have an Mvp-object on which machine learning pipeline can be applied:

import joblib
from sklearn.preprocessing import StandardScaler
from sklearn.svm import SVC
from sklearn.pipeline import Pipeline
from sklearn.model_selection import StratifiedKFold
from sklearn.metrics import accuracy_score, f1_score
from skbold.feature_selection import fisher_criterion_score, SelectAboveCutoff
from skbold.feature_extraction import RoiIndexer
from skbold.postproc import MvpResults

mvp = joblib.load('~/mvp_sub001.jl')
roiindex = RoiIndexer(mvp=mvp,
                      lateralized=False)  # loads in bilateral mask

# Extract amygdala patterns from whole-brain
mvp.X =

# Define pipeline
pipe = Pipeline([
    ('scaler', StandardScaler()),
    ('anova', SelectAboveCutoff(fisher_criterion_score, cutoff=5)),
    ('svm', SVC(kernel='linear'))

cv = StratifiedKFold(y=mvp.y, n_splits=5)

# Initialization of MvpResults; 'forward' indicates that it keeps track of
# the forward model corresponding to the weights of the backward model
# (see Haufe et al., 2014, Neuroimage)
mvp_results = MvpResults(mvp=mvp, n_iter=len(cv), feature_scoring='forward',
                         f1=f1_score, accuracy=accuracy_score)

for train_idx, test_idx in cv.split(mvp.X, mvp.y):

    train, test = mvp.X[train_idx, :], mvp.X[test_idx, :]
    train_y, test_y = mvp.y[train_idx], mvp.y[train_idx], train_y)
    pred = pipe.predict(test)

    mvp_results.update(test_idx, pred, pipeline=pipe) # update after each fold!

mvp_results.compute_scores() # compute!
mvp_results.write(out_path) # write file with metrics and niftis with feature-scores!

An example workflow: MvpBetween

Suppose you have MRI data from a large set of subjects (let’s say >50), including (task-based) functional MRI, structural MRI (T1-weighted images, DTI), and behavioral data (e.g. questionnaires, behavioral tasks). Such a dataset would qualify for a between subject decoding analysis using the MvpBetween object. To use the MvpBetween functionality effectively, it is important that the data is organized sensibly. An example is given below.


In this example, each subject has three different data-sources: two FEAT- directories (with functional contrasts) and one VBM-file. Let’s say that we’d like to use all of these sources of information together to predict some behavioral variable, neuroticism for example (as measured with e.g. the NEO-FFI). The most important argument passed to MvpBetween is source. This variable, a dictionary, should contain the data-types you want to extract and their corresponding paths (with wildcards at the place of subject-specific parts):

import os
from skbold import roidata_path
gm_mask = os.path.join(roidata_path, 'GrayMatter.nii.gz')

source = dict(
    Contrast_t1cope1={'path': '~/Project_dir/sub*/Task1.feat/cope1.nii.gz'},
    Contrast_t2cope2={'path': '~/Project_dir/sub*/Task2.feat/cope2.nii.gz'},
    VBM={'path': '~/Project_dir/sub*/vbm.nii.gz', 'mask': gm_mask}

Now, to initialize the MvpBetween object, we need some more info:

from skbold.core import MvpBetween

subject_idf='sub-0??' # this is needed to extract the subject names to
                      # cross-reference across data-sources

subject_list=None     # can be a list of subject-names to include

mvp = MvpBetween(source=source, subject_idf=subject_idf, mask=None,

# like with MvpWithin, you can simply call create() to start the extraction!

# and write to disk using write()
mvp.write(path='~/', name='mvp_between') # saves to disk!

This is basically all you need to create a MvpBetween object! It is very similar to MvpWithin in terms of attributes (including X, y, and various meta-data attributes). In fact, MvpResults works exactly in the same way for MvpWithin and MvpBetween! The major difference is that MvpResults keeps track of the feature-information for each feature-set separately and writes out a summarizing nifti-file for each feature-set. Transformers also work the same for MvpBetween objects/data, with the exception of the cluster-threshold transformer.